#305 Handle z-line problem in .ms2 files more gracefully

[William S Noble]

I converted files from RAW to ms2 using proteowizard, and the S line and Z lines were inconsistent. The S line contains the proper value, so I only get reasonable results if I run tide-index using the "use-z-line=F" option. There should be a better way to handle this.

Here is a sample header from the MS2 file:

S 3 3 618.31
I RTime 0.009321613
I BPI 1355.01
I BPM 609.2901
I TIC 13412.81
Z 2 1234.596

[William S Noble]

Jeff pointed out that sometimes the S and Z lines should not agree. This would occur, for instance, when a method like Bullseye has been used to process the file. So the warning message should read something like this:

"INFO: In the file foo.ms2, Crux has detected a disagreement between the precursor m/z value in the S line and the corresponding mass in the Z line. This disagreement might be OK, if it was introduced by preprocessing the file using a tool such as Bullseye. But if you have not performed such preprocessing, then you might want to consider setting the use-z-line parameter to F."

[Jeff Howbert]

The S and Z lines in Bill's example do not agree. As a reminder, the mass on the S line is the observed m/z of the precursor, and the mass on the Z line is [ neutral mass of the precursor + mass of H+ ], assuming the precursor charge state listed on the Z line. In this case the S line m/z should give a Z line mass of 1235.613 for charge state 2.

I'm pretty confident this is a result of the same problem I noted quite some time ago, that occurs when MSconvert creates .ms2 files from other formats. It apparently was never fixed.

[Kaipo]

In the pwiz code it's calculated by this function:

double calculateMass(double mz, int charge)
{
    return (mz * charge) - (charge * Proton);
}

I guess it should be:
(mz * charge) - ((charge - 1) * Proton)
?

[Jeff Howbert]

Hi Kaipo,

The new formula you propose is correct.

Jeff

On Fri, 21 Aug 2015, Kaipo wrote:

In the pwiz code it's calculated by this function:
~~~~~
double calculateMass(double mz, int charge)
{
return (mz * charge) - (charge * Proton);
}
~~~~~
I guess it should be:
(mz * charge) - ((charge - 1) * Proton)
?

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** [issues:#305] Handle z-line problem in .ms2 files more gracefully**

Status: open
Milestone: post v2.0
Created: Thu Aug 20, 2015 05:31 PM UTC by William S Noble
Last Updated: Thu Aug 20, 2015 06:27 PM UTC
Owner: William S Noble

I converted files from RAW to ms2 using proteowizard, and the S line and Z lines were inconsistent. The S line contains the proper value, so I only get reasonable results if I run tide-index using the "use-z-line=F" option. There should be a better way to handle this.

Here is a sample header from the MS2 file:

S 3 3 618.31
I RTime 0.009321613
I BPI 1355.01
I BPM 609.2901
I TIC 13412.81
Z 2 1234.596

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